For Everyone,
Print out the article, read a few times, answer Study Q's
Bring the printed article and your completed Study Q's to class.
5th Paper
- use PubMed to download the PDF
If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network Mochalkin, I.; Miller, J.; Narasimhan, L.; Thanabal, V.; Erdman, P.; Cox, P.; Prasad, J.; Lightle, S.; Huband, M.; Stover, C., Discovery of antibacterial biotin carboxylase inhibitors by virtual screening and fragment-based approaches. ACS Chem Biol2009,4 (6), 473-83. Study Q's: answer these and bring paper copy to class. They can be found in: Google Drive/JournalClub
On Friday, meet with a mentor or Dr. B to go over your slides and discuss
On Monday (or maybe Tuesday), meet with Dr. B to go over the final version of your slides in preparation for presenting in class
Upload your final presentation at least 1 hour before class to the GroupMeetingSlides/GroupMeetingSlides/StudentPresentations folder on Google Docs
RESEARCH PRESENTATIONS INSTRUCTIONS (see tips below)
Prepare a draft of your slides
On Friday, meet with a mentor or Dr. B to go over your slides and discuss
On Monday (or maybe Tuesday), meet with Dr. B to go over the final version of your slides in preparation for presenting in class
Upload your final presentation at least 1 hour before class to the GroupMeetingSlides/GroupMeetingSlides/StudentPresentations folder on Google Docs
JOURNAL CLUB PRESENTATIONS INSTRUCTIONS (see tips below)
On Friday, meet with Dr. B to go over initial questions about the paper (read it at least once beforehand)
Prepare a draft of your slides
On Monday - meet with Dr. B to go over your slides and discuss in person
Tuesday (maybe meet again to go over final version)
Upload your final presentation at least 1 hour before class to the GroupMeetingSlides/GroupMeetingSlides/StudentPresentations folder on Google Docs
Guidelines (for all presentations):
prepare a 10 minute powerpoint slide show
Start out with a title slide that has:
Put YOUR name on title slide also since you are presenting.
Put the date of the presentation on their as well - and something like 'VDS Summer Journal Club' or 'VDS Technical Presentation' or the a title for your research if doing a Research Presentation
for Journal Club presentations, include the: Journal Article name, Journal Name and Authors on it.
Display your enthusiasm about the work you are presenting. Enthusiasm is contagious, and keeps your audience interested. Can you think of anything to make your presentation unique? An unusual prop or visual aid? Make your presentation "professional". That means, stand up in front, look directly at your audience, and don't "read" your slides.
Go through your talk at least once as a practice run
TIPS:
for best contrast and readability - use black text on white background.
Put date on the title slide
When you get to a figure, explain what is on the X axis and what is on the Y-axis. This helps them understand the graph and also gives a little time for them to view the graph and digest what is being shown.
For graphs and tables - be sure to explicitly state what the 'take home message' of that figure is. What does the graph tell the reader?
Guidelines (for all Journal Club presentations specifically):
Create an introduction that provides a broad perspective for the specific [[#|work]] being presented. For example, if you are presenting a [[#|paper]] on a new protein, you should provide some background on the protein family and what it does. Don't assume that everyone in your audience knows the background. You can use your own content if you like - along with that given by the authors.
Include a picture or image that helps give a visual for the background.
Include any statistics about the disease and its prevalence (this is motivation)
Instead of simply describing the methods used, look at the methods critically, with an eye for anything interesting or unusual. Point out anything that might be generally useful. For example, did the authors use any techniques that we are currently using in our lab?
Include graphs and figures from the paper.Use the SNIPPING tool in Windows to get pictures of the graphs, etc. from the paper. However, you will want a few 'original' images of your own. You can also make your own cartoons and schematic diagrams or show relevant pictures to get across the point.
Make an effort to explain what is going on in the figures (try to include all of them - but you can leave out some if they do not contribute to a 10 minute presentation)
Be sure to actually show the images and figures from the paper when talking about them (include some type of caption)
Do the results suggest any additional experiments that would be the next.?
Feel free to interject your own viewpoint of the research (is it valuable, did they do anything you liked or disliked?)
Clearly explain the significance of the results. Results by themselves are dull, unless they have significance. The significance may not be obvious to the audience, so point it out specifically.
What is the most significant contribution of the specific work to the field in general?
Tips for making your Research Presentations
use colors with good contrast (i.e. not light blue on lighter blue!)
put date of presentation on Title slide
number the slides (use the Insert >> Slide Number in powerpoint)
Italicize organism name and lower case the species name. e.g.: Rickettsia prowazekii
Start out with Motivation slides
Introduction to disease and/or special techniques
Intro about protein target
-(include EC number, reaction diagram from Brenda (use Snipping tool to image), etc)
-If you have a crystal structure of your protein - make your own PyMol image and show it.
Slide on Objective - what are you setting out to do in THIS project
Overview of procedures (e.g. explain cloning procedure in general, or protein expression, purification,characterization)
-- want this to be a broad view of the procedures.
FOR CLONING SLIDES:
Include the length of your gene (the CDS) and include the %GC content. - that helps to tell if your target is 'easy'
Include the diagram from the Overlap OCR protocol that shows the schematic of how it works.
and Include an image of pNIC-Bsa4 (from the PDF online) when you talk about expression vectors and cloning into it.
Label your gel lanes and marker with Text Boxes & Arrows (not just a legen on the side that is hard to read)
Show a Nanodrop images of your PCR cleanup or MidiPrep yields of quantity
Save file with the target name and your initials and date in the filename.
upload final version to GDocs/GroupMeetingSlides/StudentPresentations
Reading Strategies for Journal Articles
First pass
- Skim Abstract, Conclusions, Figures Second pass
- Read Introduction, Methods, Results
---- Underline – only up to 10%
---- Make notes in margin, draw sketches
- Look up reaction mechanism of enzyme
- Circle unfamiliar words
------- Then go back afterwards and look up definitions
Take a break (couple of hours - to a day or so)
- Coffee break !
Third pass
- Read for comprehension
6th Paper
- use PubMed to download the PDF
If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network
Henriksson, L. M.; Unge, T.; Carlsson, J.; Aqvist, J.; Mowbray, S. L.; Jones, T. A., Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis. J Biol Chem2007,282 (27), 19905-16. Study Q's: answer these and bring paper copy to class. They can be found in: Google Drive/JournalClub
7th Paper
Hu, X.; Vujanac, M.; Southall, N.; Stebbins, C. E., Inhibitors of the Yersinia protein tyrosine phosphatase through high throughput and virtual screening approaches. Bioorg Med Chem Lett2013, 23 (4), 1056-62. HuYopHVirtualBioorgMedChemLett2013.pdf
Study Q's: answer these and bring paper copy to class. They can be found in: Google Drive/JournalClub
1st Journal Club Fall 2015
1st Paper Kovac, A.; Konc, J.; Vehar, B.; Bostock, J.; Chopra, I.; Janezic, D.; Gobec, S., Discovery of new inhibitors of D-alanine:D-alanine ligase by structure-based virtual screening. J Med Chem2008,51 (23), 7442-8. KovacDalanineDalanineLigaseVirtualScreenJMedChem2008.pdf
Study Q's: answer these and bring paper copy to class. They can be found in: Google Drive/JournalClub
2nd Paper
Tomlinson, S.; Malmstrom, R.; Watowich, S., New approaches to structure-based discovery of dengue protease inhibitors. Infect Disord Drug Targets2009,9 (3), 327-43.
- use PubMed to download the PDF
If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network Study Q's: answer these and bring paper copy to class. They can be found in: Google Drive/JournalClub
3rd Paper
- use PubMed to download the PDF
If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network Bai, Y.; Watt, B.; Wahome, P.; Mantis, N.; Robertus, J., Identification of new classes of ricin toxin inhibitors by virtual screening. Toxicon2010,56 (4), 526-34. Study Q's: answer these and bring paper copy to class. They can be found in: Google Drive/JournalClub
4th Paper
- use PubMed to download the PDF
If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network
A Novel Small-Molecule Inhibitor of the Avian Influenza H5N1 Virus Determined through
Computational Screening against the Neuraminidase. Jianghong An, Davy C. W. Lee, Anna H.Y. Law, Cindy L.H. Yang, Leo L.M. Poon, Allan S.Y. Lau, and
Steven J.M. Jones J. Med. Chem.2009,52, 2667–2672 Study Q's: answer these and bring paper copy to class. They can be found in: Google Drive/JournalClub
*
Hey VDSers,
Here is a link to a VDS class Mendeley account. This website will enable students to access the papers and create bibliographies. You have the option of downloading a desktop version or using the website for journal article access.
The username is vdsclass@gmail.com and the password is the same as usual (not the GDocs one - but the one to get on to the laptops in the lab. p............ ).
*
Potential Papers:
Li, Z.; Garner, A. L.; Gloeckner, C.; Janda, K. D.; Carlow, C. K., Targeting the Wolbachia cell division protein FtsZ as a new approach for antifilarial therapy. PLoS Negl Trop Dis2011,5 (11), e1411.
Henriksson, L. M.; Unge, T.; Carlsson, J.; Aqvist, J.; Mowbray, S. L.; Jones, T. A., Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis. J Biol Chem2007,282 (27), 19905-16.
Sacchettini, J.; Rubin, E.; Freundlich, J., Drugs versus bugs: in pursuit of the persistent predator Mycobacterium tuberculosis. Nat Rev Microbiol2008, 6 (1), 41-52.
Print out the article, read a few times, answer Study Q's
Bring the printed article and your completed Study Q's to class.
5th Paper
- use PubMed to download the PDF
If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network
Mochalkin, I.; Miller, J.; Narasimhan, L.; Thanabal, V.; Erdman, P.; Cox, P.; Prasad, J.; Lightle, S.; Huband, M.; Stover, C., Discovery of antibacterial biotin carboxylase inhibitors by virtual screening and fragment-based approaches. ACS Chem Biol 2009, 4 (6), 473-83.
Study Q's: answer these and bring paper copy to class. They can be found in: Google Drive/JournalClub
For Order of Presenters,
- see the Schedule Fall15
TECHNICAL PRESENTATIONS INSTRUCTIONS
RESEARCH PRESENTATIONS INSTRUCTIONS (see tips below)
JOURNAL CLUB PRESENTATIONS INSTRUCTIONS (see tips below)
Guidelines (for all presentations):
Guidelines (for all Journal Club presentations specifically):
Tips for making your Research Presentations
use colors with good contrast (i.e. not light blue on lighter blue!)
put date of presentation on Title slide
number the slides (use the Insert >> Slide Number in powerpoint)
Italicize organism name and lower case the species name. e.g.: Rickettsia prowazekii
Start out with Motivation slides
Introduction to disease and/or special techniques
Intro about protein target
-(include EC number, reaction diagram from Brenda (use Snipping tool to image), etc)
-If you have a crystal structure of your protein - make your own PyMol image and show it.
Slide on Objective - what are you setting out to do in THIS project
Overview of procedures (e.g. explain cloning procedure in general, or protein expression, purification,characterization)
-- want this to be a broad view of the procedures.
FOR CLONING SLIDES:
Include the length of your gene (the CDS) and include the %GC content. - that helps to tell if your target is 'easy'
Include the diagram from the Overlap OCR protocol that shows the schematic of how it works.
and Include an image of pNIC-Bsa4 (from the PDF online) when you talk about expression vectors and cloning into it.
Label your gel lanes and marker with Text Boxes & Arrows (not just a legen on the side that is hard to read)
Show a Nanodrop images of your PCR cleanup or MidiPrep yields of quantity
Save file with the target name and your initials and date in the filename.
upload final version to GDocs/GroupMeetingSlides/StudentPresentations
Reading Strategies for Journal Articles
First pass
- Skim Abstract, Conclusions, Figures
Second pass
- Read Introduction, Methods, Results
---- Underline – only up to 10%
---- Make notes in margin, draw sketches
- Look up reaction mechanism of enzyme
- Circle unfamiliar words
------- Then go back afterwards and look up definitions
Take a break (couple of hours - to a day or so)
- Coffee break !
Third pass
- Read for comprehension
6th Paper
- use PubMed to download the PDF
If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network
Henriksson, L. M.; Unge, T.; Carlsson, J.; Aqvist, J.; Mowbray, S. L.; Jones, T. A., Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis. J Biol Chem 2007, 282 (27), 19905-16.
Study Q's: answer these and bring paper copy to class. They can be found in: Google Drive/JournalClub
7th Paper
Hu, X.; Vujanac, M.; Southall, N.; Stebbins, C. E., Inhibitors of the Yersinia protein tyrosine phosphatase through high throughput and virtual screening approaches. Bioorg Med Chem Lett 2013, 23 (4), 1056-62.
HuYopHVirtualBioorgMedChemLett2013.pdf
Supplement:
HuYopHVirtualBioorgMedChemLett2013mmc1_SUPPLEMENT.docx
Study Q's: answer these and bring paper copy to class. They can be found in: Google Drive/JournalClub
1st Journal Club Fall 2015
1st Paper
Kovac, A.; Konc, J.; Vehar, B.; Bostock, J.; Chopra, I.; Janezic, D.; Gobec, S., Discovery of new inhibitors of D-alanine:D-alanine ligase by structure-based virtual screening. J Med Chem 2008, 51 (23), 7442-8.
KovacDalanineDalanineLigaseVirtualScreenJMedChem2008.pdf
Study Q's: answer these and bring paper copy to class. They can be found in: Google Drive/JournalClub
2nd Paper
Tomlinson, S.; Malmstrom, R.; Watowich, S., New approaches to structure-based discovery of dengue protease inhibitors. Infect Disord Drug Targets 2009, 9 (3), 327-43.
- use PubMed to download the PDF
If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network
Study Q's: answer these and bring paper copy to class. They can be found in: Google Drive/JournalClub
3rd Paper
- use PubMed to download the PDF
If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network
Bai, Y.; Watt, B.; Wahome, P.; Mantis, N.; Robertus, J., Identification of new classes of ricin toxin inhibitors by virtual screening. Toxicon 2010, 56 (4), 526-34.
Study Q's: answer these and bring paper copy to class. They can be found in: Google Drive/JournalClub
4th Paper
- use PubMed to download the PDF
If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network
A Novel Small-Molecule Inhibitor of the Avian Influenza H5N1 Virus Determined through
Computational Screening against the Neuraminidase. Jianghong An, Davy C. W. Lee, Anna H.Y. Law, Cindy L.H. Yang, Leo L.M. Poon, Allan S.Y. Lau, and
Steven J.M. Jones J. Med. Chem. 2009, 52, 2667–2672
Study Q's: answer these and bring paper copy to class. They can be found in: Google Drive/JournalClub
*
Hey VDSers,
Here is a link to a VDS class Mendeley account. This website will enable students to access the
papers and create bibliographies. You have the option of downloading a desktop version or using the
website for journal article access.
http://www.mendeley.com/
The username is vdsclass@gmail.com and the password is the same as usual (not the GDocs one - but the one to get on to the laptops in the lab. p............ ).
*
Potential Papers:
Li, Z.; Garner, A. L.; Gloeckner, C.; Janda, K. D.; Carlow, C. K., Targeting the Wolbachia cell division protein FtsZ as a new approach for antifilarial therapy. PLoS Negl Trop Dis 2011, 5 (11), e1411.Henriksson, L. M.; Unge, T.; Carlsson, J.; Aqvist, J.; Mowbray, S. L.; Jones, T. A., Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis. J Biol Chem 2007, 282 (27), 19905-16.
Sacchettini, J.; Rubin, E.; Freundlich, J., Drugs versus bugs: in pursuit of the persistent predator Mycobacterium tuberculosis. Nat Rev Microbiol 2008, 6 (1), 41-52.